AMBER Archive (2008)

Subject: Re: AMBER: bellymask for DNA backbone doesn't seem to work

From: Thomas Cheatham III (tec3_at_utah.edu)
Date: Thu Jul 03 2008 - 15:40:47 CDT

> This works fine. But when I do:
>
> ibelly=1,
> bellymask=@P, C5', C4', C3', O5', O3'

...you need to put quotes around it (which would normally be ' ' but
since you have ' in the atom names, I would use " ":

 bellymask="@P, C5', C4', C3', O5', O3'",

Note also that IF you happen to be using belly on more than one molecule
(for example duplex DNA) and running constant pressure, the pressure
scaling code will shift the belly coordinates which is undesirable at this
will move your belly atoms. To get around this, you need to hack the
prmtop to put the two strands into a single molecule)...

--tec3

p.s. how to hack the prmtop?

(1) edit prmtop, search for "MOL"

(2) move to the line above and you will see 3 numbers. Decrement the 2nd
and 3rd by 1.

(3) move down to the ATOMS_PER_MOLECULE SECTION. Add the first two
numbers (i.e. the number of atoms in the first two molecules) and use this
to replace the first numbers. Shift all the numbers by one, i.e. if ions
are next, replace the second number with 1, replace the final 1 with 3
(for the water) and delete the final 3 (easiest to get there by searching
for % and going back up).

[This is described in one of the old tutorials too...]

Here is a diff on one of my recent hacks to do this:

<sanddune 15> diff -C 2 prmtop ../angle2/

*** prmtop 2007-05-07 17:11:41.000000000 -0600
--- ../angle2/prmtop 2008-07-02 16:37:28.000000000 -0600
***************
*** 101214,101221 ****
  %FLAG SOLVENT_POINTERS
  %FORMAT(3I8)
! 610 15644 146
  %FLAG ATOMS_PER_MOLECULE
  %FORMAT(10I8)
! 7555 18 1 1 1 1 1 1 1 1
         1 1 1 1 1 1 1 1 1 1
         1 1 1 1 1 1 1 1 1 1
--- 101214,101221 ----
  %FLAG SOLVENT_POINTERS
  %FORMAT(3I8)
! 610 15643 145
  %FLAG ATOMS_PER_MOLECULE
  %FORMAT(10I8)
! 7573 1 1 1 1 1 1 1 1 1
         1 1 1 1 1 1 1 1 1 1
         1 1 1 1 1 1 1 1 1 1
***************
*** 101231,101235 ****
         1 1 1 1 1 1 1 1 1 1
         1 1 1 1 1 1 1 1 1 1
! 1 1 1 1 1 3 3 3 3 3
         3 3 3 3 3 3 3 3 3 3
         3 3 3 3 3 3 3 3 3 3
--- 101231,101235 ----
         1 1 1 1 1 1 1 1 1 1
         1 1 1 1 1 1 1 1 1 1
! 1 1 1 1 3 3 3 3 3 3
         3 3 3 3 3 3 3 3 3 3
         3 3 3 3 3 3 3 3 3 3
***************
*** 102781,102785 ****
         3 3 3 3 3 3 3 3 3 3
         3 3 3 3 3 3 3 3 3 3
! 3 3 3 3
  %FLAG BOX_DIMENSIONS
  %FORMAT(5E16.8)
--- 102781,102785 ----
         3 3 3 3 3 3 3 3 3 3
         3 3 3 3 3 3 3 3 3 3
! 3 3 3
  %FLAG BOX_DIMENSIONS
  %FORMAT(5E16.8)

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